Licensed games can appear on the Virtual Console providing that the developers of the original game still have the license today or are willing to aquire it. Thats the way I understand it anyway.

And another hurdle is that only Nintendo published games are appearing on the N64 at the moment (even if a third party developed the game for them, i.e. Cruis'n USA). Nobody seems to know if third party publishers are restricted from putting their N64 games on the VC or if they just have no interest in doing so. Granted this is something that could change in the near future but we'll never know when exactly until we find out.